Monitoring communities of fish is important for the management and sustainability of fisheries and marine ecosystems. Baited remote underwater video systems (BRUVs) are among the most effective ...nondestructive techniques for sampling bony fishes and elasmobranchs (sharks, rays, and skates). However, BRUVs sample visually conspicuous biota; hence, some taxa are undersampled or not recorded at all. We compared the diversity of fishes characterized using BRUVs with diversity detected via environmental DNA (eDNA) metabarcoding. We sampled seawater and captured BRUVs imagery at 48 locales that included reef and seagrass beds inside and outside a marine reserve (Jurien Bay in Western Australia). Eighty‐two fish genera from 13 orders were detected, and the community of fishes described using eDNA and BRUVs combined yielded >30% more generic richness than when either method was used alone. Rather than detecting a homogenous genetic signature, the eDNA assemblages mirrored the BRUVs’ spatial explicitness; differentiation of taxa between seagrass and reef was clear despite the relatively small geographical scale of the study site (∼35 km2). Taxa that were not sampled by one approach, due to limitations and biases intrinsic to the method, were often detected with the other. Therefore, using BRUVs and eDNA in concert provides a more holistic view of vertebrate marine communities across habitats. Both methods are noninvasive, which enhances their potential for widespread implementation in the surveillance of marine ecosystems.
Uso Combinado del Metacódigo de Barras de eDNA y Videograbaciones para la Evaluación de la Biodiversidad de Peces
Resumen
El monitoreo de comunidades de peces es importante para el manejo y sustentabilidad de las pesquerías y los ecosistemas marinos. Los sistemas remotos de video submarino con carnada (SRVSC) están entre las técnicas no destructivas más efectivas para el muestreo de peces óseos y elasmobranquios (tiburones, mantarrayas y rayas). Sin embargo, los SRVSC muestrean biota que es conspicua visiblemente; entonces, algunos taxones están mal muestreados o simplemente no se registran en los muestreos. Comparamos la diversidad de peces caracterizada usando SRVSC con la diversidad detectada por medio del metacódigo de barras de ADN ambiental (eDNA, en inglés). Muestreamos el agua de mar y capturamos imágenes con SRVSC en 48 localidades que incluyeron el arrecife y los pastos marinos dentro y fuera de una reserva marina (Bahía Jurien en el oeste de Australia). Se detectaron 83 géneros de peces de 13 órdenes, y la comunidad de peces descrita con el uso combinado del eDNA y el SRVSC produjo >30% riqueza más genérica que cuando cualquiera de los dos métodos se usó individualmente. En lugar de detectar una firma genética homogénea, los ensamblados de eDNA reflejaron la claridad espacial del SRVSC; la diferenciación de los taxones entre los pastos marinos y el arrecife fue clara a pesar la escala geográfica relativamente pequeña del sitio de estudio (∼35 km2). Los taxones que no fueron muestreados por uno de los métodos, por causa de limitaciones y sesgos intrínsecos al método, casi siempre fueron detectados usando el otro método. Por lo tanto, el uso de SRVSC y el eDNA en concreto proporciona una visión más holística de las comunidades marinas de vertebrados en todos los hábitats. Ambos métodos son no invasivos, lo que incrementa su potencial para ser una implementación de uso amplio en la vigilancia de los ecosistemas marinos.
Article impact statement: Use of video and environmental genomics in conservation will greatly improve capacity to effectively monitor fish biodiversity.
Marine ecosystems are changing rapidly as the oceans warm and become more acidic. The physical factors and the changes to ocean chemistry that they drive can all be measured with great precision. ...Changes in the biological composition of communities in different ocean regions are far more challenging to measure because most biological monitoring methods focus on a limited taxonomic or size range. Environmental DNA (eDNA) analysis has the potential to solve this problem in biological oceanography, as it is capable of identifying a huge phylogenetic range of organisms to species level. Here we develop and apply a novel multi-gene molecular toolkit to eDNA isolated from bulk plankton samples collected over a five-year period from a single site. This temporal scale and level of detail is unprecedented in eDNA studies. We identified consistent seasonal assemblages of zooplankton species, which demonstrates the ability of our toolkit to audit community composition. We were also able to detect clear departures from the regular seasonal patterns that occurred during an extreme marine heatwave. The integration of eDNA analyses with existing biotic and abiotic surveys delivers a powerful new long-term approach to monitoring the health of our world's oceans in the context of a rapidly changing climate.
This study comprised a meta-analysis of elasmobranch bycatch in commercial longline, trawl, purse-seine and gillnet fisheries in order to obtain a general perspective of bycatch patterns, and to ...expose knowledge gaps and identify management and research priorities. Two bycatch ratios were considered: the number and the weight of elasmobranch bycatch relative to that of the target species captured. Patterns were determined through machine learning algorithms with gear type, oceanic region, habitat and the presence or absence of bycatch management measures as candidate predictors. There are considerable information gaps. Most of the current information on elasmobranch bycatch is for the North Atlantic, which is not where the greatest fishing pressure is exerted, so several fisheries were largely under-represented. Overall for sharks, gear type was the most important predictor with pelagic longline fisheries in the South Atlantic displaying the highest bycatch ratios. No patterns were found for ray bycatch ratios. For the fisheries considered in this study, pelagic longlines, and deep-sea and coastal trawl fisheries had the largest total annual shark and ray bycatch, respectively. Blue sharks (Prionace glauca, Carcharhinidae) dominated the total annual bycatch of longline fisheries. For other fishing gears, the annual species-specific bycatch composition varied across oceanic regions. Many of the fisheries with the largest elasmobranch bycatch operate over large spatial scales and often in international waters. International management, mitigation and cooperation are an essential component for the sustainability of elasmobranch bycatch species. Data collection systems and data availability are required at a global scale to improve assessments of elasmobranch bycatch and this should be a high priority for ongoing management and monitoring.
•The gear type of a particular fishery was the most important predictor variable for shark bycatch ratios.•Pelagic longline fisheries had the highest shark bycatch ratios.•Deep-sea trawl and pelagic longline fisheries caught the largest quantity of rays and sharks, respectively.•Substantial information gaps exist in elasmobranch bycatch data complicating global analyses.
Ecosystem reconfigurations arising from climate-driven changes in species distributions are expected to have profound ecological, social, and economic implications. Here we reveal a rapid ...climate-driven regime shift of Australian temperate reef communities, which lost their defining kelp forests and became dominated by persistent seaweed turfs. After decades of ocean warming, extreme marine heat waves forced a 100-kilometer range contraction of extensive kelp forests and saw temperate species replaced by seaweeds, invertebrates, corals, and fishes characteristic of subtropical and tropical waters. This community-wide tropicalization fundamentally altered key ecological processes, suppressing the recovery of kelp forests.
Climate‐mediated changes to biotic interactions have the potential to fundamentally alter global ecosystems. However, the capacity for novel interactions to drive or maintain transitions in ecosystem ...states remains unresolved. We examined temperate reefs that recently underwent complete seaweed canopy loss and tested whether a concurrent increase in tropical herbivores could be maintaining the current canopy‐free state. Turf‐grazing herbivorous fishes increased in biomass and diversity, and displayed feeding rates comparable to global coral reefs. Canopy‐browsing herbivores displayed high (~ 10 000 g 100 m⁻²) and stable biomass between 2006 and 2013. Tropical browsers had the highest abundance in 2013 and displayed feeding rates approximately three times higher than previously observed on coral reefs. These observations suggest that tropical herbivores are maintaining previously kelp‐dominated temperate reefs in an alternate canopy‐free state by grazing turfs and preventing kelp reestablishment. This remarkable ecosystem highlights the sensitivity of biotic interactions and ecosystem stability to warming and extreme disturbance events.
Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a ...growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate‐related threats and as such there is a pressing need for cost‐effective whole‐ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high‐resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)—a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140 km2 area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management.
Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. ...Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using 'tree of life' (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing 'universal' PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs.
Effective biomonitoring is critical for driving management outcomes that ensure long‐term sustainability of the marine environment. In recent years, environmental DNA (eDNA), coupled with ...metabarcoding methodologies, has emerged as a promising tool for generating biotic surveys of marine ecosystems, including those under anthropogenic pressure. However, more empirical data are needed on how to best implement eDNA field sampling approaches to maximize their utility for each specific application. The effect of the substrate chosen for eDNA sampling on the diversity of marine taxa detected by DNA metabarcoding has not yet been systematically analysed, despite aquatic systems being those most commonly targeted for eDNA studies. We investigated the effect of four commonly used eDNA substrates to explore taxonomic diversity: (a) surface water, (b) marine sediment, (c) settlement plates and (d) planktonic tows. With a focus on coastal ports, 332 eDNA samples from Australia (Indian and Southern oceans) and Kazakhstan (Caspian Sea) were collected and analysed by multi‐assay DNA metabarcoding. Across study locations, between 30% and 52% of eukaryotic families detected were unique to a particular substrate and <6% of families were found in all four substrates. Taxonomic composition varied significantly depending on the substrate sampled implying that the suitability (and bias) of an eDNA substrate will depend on the focal taxa. These findings demonstrate that single substrate eDNA metabarcoding likely underestimates the total eukaryotic diversity. Future eDNA experimental design should consider incorporating multiple substrates or select substrate(s) best suited to the specific detection of target taxa.
Abstract
There is a need for automatic systems that can reliably detect, track and classify fish and other marine species in underwater videos without human intervention. Conventional computer vision ...techniques do not perform well in underwater conditions where the background is complex and the shape and textural features of fish are subtle. Data-driven classification models like neural networks require a huge amount of labelled data, otherwise they tend to over-fit to the training data and fail on unseen test data which is not involved in training. We present a state-of-the-art computer vision method for fine-grained fish species classification based on deep learning techniques. A cross-layer pooling algorithm using a pre-trained Convolutional Neural Network as a generalized feature detector is proposed, thus avoiding the need for a large amount of training data. Classification on test data is performed by a SVM on the features computed through the proposed method, resulting in classification accuracy of 94.3% for fish species from typical underwater video imagery captured off the coast of Western Australia. This research advocates that the development of automated classification systems which can identify fish from underwater video imagery is feasible and a cost-effective alternative to manual identification by humans.
In recent decades, spearfishing with SCUBA has emerged as an efficient method for targeting reef fish in deeper waters. However, deeper waters are increasingly recognised as a potential source of ...refuge that may help sustain fishery resources. We used a combination of historical catch data over a 20-year time period and fishery-independent surveys to investigate the effects of SCUBA spearfishing on coral reef fish populations in the southern Mariana Islands. Two jurisdictions were studied; Guam, where SCUBA spearfishing is practiced, and the nearby Commonwealth of Northern Mariana Islands (CNMI), where SCUBA spearfishing has been banned since 2003. Fishery-independent data were collected using baited remote underwater stereo-video systems (stereo-BRUVs) stratified by depth, marine protected area status and jurisdiction. Herbivores (primary consumers) dominated spearfishing catches, with parrotfish (scarines) and surgeonfish/unicornfish (acanthurids) the main groups harvested. However, the large, endangered humphead wrasse (Cheilinus undulatus) was the main species by weight landed by SCUBA spearfishers. SCUBA spearfishing was associated with declining size of scarines over time and catches shifting from a dominance of large parrotfishes to a mixed assemblage with increasing proportions of acanthurids. Comparisons between Guam and the nearby CNMI revealed differences in the assemblage of fished species and also greater size of scarines and acanthurids in deep water where SCUBA fishing is banned. These results suggest that SCUBA spearfishing impacts reef fish populations and that the restriction of this fishing method will ensure refuge for fish populations in deeper waters. We recommend a ban on SCUBA spearfishing to preserve or aid the recovery of large, functionally important coral reef species and to improve the sustainability of coral reef fisheries.
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